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zellerlab / stag

A hierarchical taxonomic classifier for metagenomic sequences
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alignment using proteins instead of genes #3

Closed AlessioMilanese closed 4 years ago

AlessioMilanese commented 4 years ago

It can be that it's better to align with protein sequences and then transform this into gene alignments (for example if you have a hmm model for the protein alignments and not the genes). Would be good to add this option.

AlessioMilanese commented 4 years ago

Done in 8df3d97. With the -p option, it will align the protein sequences provided by -p, and then convert the multiple sequence alignment of the protein into the gene sequences provided by -i. Note that we require to have the same order of sequences. The name of the id produced is the one from the genes (so it uses the gene id in the fasta file provided in -i).